Parallelized computational 3D video microscopy of freely moving organisms at multiple gigapixels per second

To study the behavior of freely moving model organisms such as zebrafish (Danio rerio) and fruit flies (Drosophila) across multiple spatial scales, it would be ideal to use a light microscope that can resolve 3D information over a wide field of view (FOV) at high speed and high spatial resolution. However, it is challenging to design an optical instrument to achieve all of these properties simultaneously. Existing techniques for large-FOV microscopic imaging and for 3D image measurement typically require many sequential image snapshots, thus compromising speed and throughput. Here, we present 3D-RAPID, a computational microscope based on a synchronized array of 54 cameras that can capture high-speed 3D topographic videos over a 135-cm^2 area, achieving up to 230 frames per second at throughputs exceeding 5 gigapixels (GPs) per second. 3D-RAPID features a 3D reconstruction algorithm that, for each synchronized temporal snapshot, simultaneously fuses all 54 images seamlessly into a globally-consistent composite that includes a coregistered 3D height map. The self-supervised 3D reconstruction algorithm itself trains a spatiotemporally-compressed convolutional neural network (CNN) that maps raw photometric images to 3D topography, using stereo overlap redundancy and ray-propagation physics as the only supervision mechanism. As a result, our end-to-end 3D reconstruction algorithm is robust to generalization errors and scales to arbitrarily long videos from arbitrarily sized camera arrays. The scalable hardware and software design of 3D-RAPID addresses a longstanding problem in the field of behavioral imaging, enabling parallelized 3D observation of large collections of freely moving organisms at high spatiotemporal throughputs, which we demonstrate in ants (Pogonomyrmex barbatus), fruit flies, and zebrafish larvae

Data from: Alien and native plant establishment in grassland communities is more strongly affected by disturbance than above- and below-ground enemies

Understanding the factors that drive commonness and rarity of plant species and whether these factors differ for alien and native species are key questions in ecology. If a species is to become common in a community, incoming propagules must first be able to establish. The latter could be determined by competition with resident plants, the impacts of herbivores and soil biota, or a combination of these factors. We aimed to tease apart the roles that these factors play in determining establishment success in grassland communities of 10 alien and 10 native plant species that are either common or rare in Germany, and from four families. In a two-year multisite field experiment, we assessed the establishment success of seeds and seedlings separately, under all factorial combinations of low vs. high disturbance (mowing vs mowing and tilling of the upper soil layer), suppression or not of pathogens (biocide application) and, for seedlings only, reduction or not of herbivores (net-cages). Native species showed greater establishment success than alien species across all treatments, regardless of their commonness. Moreover, establishment success of all species was positively affected by disturbance. Aliens showed lower establishment success in undisturbed sites with biocide application. Release of the undisturbed resident community from pathogens by biocide application might explain this lower establishment success of aliens. These findings were consistent for establishment from either seeds or seedlings, although less significantly so for seedlings, suggesting a more important role of pathogens in very early stages of establishment after germination. Herbivore exclusion did play a limited role in seedling establishment success. Synthesis: In conclusion, we found that less disturbed grassland communities exhibited strong biotic resistance to establishment success of species, whether alien or native. However, we also found evidence that alien species may benefit weakly from soilborne enemy release, but that this advantage over native species is lost when the latter are also released by biocide application. Thus, disturbance was the major driver for plant species establishment success and effects of pathogens on alien plant establishment may only play a minor role

Late endosomal/lysosomal targeting and lack of recycling of the ligand-occupied endothelin B receptor

and Cy3-ET1 fluorescences were found in the perinuclear region, colocalized with fluorescent low density lipoproteins, a marker of the late endosomal/lysosomal pathway, but not with fluorescent transferrin, a marker of the recycling pathway. No dissociation of Cy3-ET1 from the receptor was seen within 4 h. Using 125 I-ET1 or Cy3-ET1, binding sites were again demonstrable at the cell surface within 2 h. The reappearance of binding sites was abolished by prior treatment of the cells with cycloheximide, an inhibitor of protein synthesis. The data demonstrate that the ligand-occupied ET B receptor is internalized; however, it does not recycle like most of the G protein-coupled receptors but is sorted to the late endosomal/lysosomal pathway in a manner similar to that of the family of proteaseactivated receptors

Müller et al. 2016 Journal of Ecology (2) seeds

Data for establishment from seeds collected in the field for Müller et al. 2016. Columns: site (codes for the respective site); plot (codes for the respective plot in site); fungicide (biocide treatment yes/no); disturbance (disturbance treatment yes/no); x (x position within plot); y (y position within plot); species (species name); name (alternative coding for species names); origin (alien /native); Commonness (common/rare); tk25 (number of grid cells occupied in Germany); Family (species family); seedlings (number of seedlings recorded in the field); sowing density (initial number of seeds sown in the field at the respectie position

Data_Müller et al. 2016 Journal of Ecology

Data on survival of seedlings collected in the field (Müller et al. 2016). Columns: Individual (Identifier for site/plot/xyposition of each individual); Site (column for site); Plot (column for plot); Position (column for Position); Disturbance (disturbance treatment high/low); Fungicide (Biocide application yes/no); Herbivory (open / closed cage); Family (species family); Genus (species genus); Species (species name); Name(alternative abrev. for species names); Origin (alien/native); Commonness (common/rare); Grid_cells (number of grid cells occupied by the species in Germany); Planted (planting date); t_cover(date when veg. cover was recorded for the respective position); t1 (time of 1st survey); Survival_t (recorded survival yes/no 1st survey); Height_t1 (recorde plant height 1st survey); Leaves (recorded leaves 1st survey); t2 (time of 2nd survey); Survival_t2 (survival at 2nd survey); t3 (time of 3rd survey); Survival t3 (survival at 3rd survey); t4 (timing of 4th survey); dayst4_t1 (number of days between survey 1 and 4); Survival t4 (survival at 4th survey): Height_t4(plant height at 4th survey); Leaves_t4 (recorded leaves at survey4); t5 (time of 5th survey); Survival_t5 (survival at 5th survey); height_t5 (recorded plant height at t5); Leaves _t5(recorded leaves at 5th survey); forbs (fraction of forb cover); grass (fraction of grass cover); background (fraction of bare ground